BioinformatIQ: Integrating devices, data types, and bioinformatic analysis in an information management system for proteomics

F. Keith Junius1, P. Bizannes, P. Doggett, M. Harrison, B. Srinivasan, E. Shaw, M. Traini, W. McDonald, and Marc R. Wilkins, Proteome Systems

The analysis of proteins in proteomics is a challenging task. The researcher relies on a number of different approaches and tools to enable proteomic analysis, many of which are highly automated and very high-throughput. Various software tools and techniques for assisting the researcher in proteomics are available. However, a fully integrated set of bioinformatic tools for storing, manipulating, and mining the large amounts of data generated by proteomic instruments has been lacking. In order to address these needs, we have developed an integrated proteomic bioinformatics system called BioinformatIQ®. BioinformatIQ® is an enterprise-level solution for proteomic data storage and analysis that sits at the centre of ProteomIQ®, a high-throughput platform for proteome analysis combining technology for sample preparation, image analysis, protein processing, and mass spectrometry. BioinformatIQ® serves as a LIMS (Laboratory Information Management System) and an electronic lab book, recording every step of an experiment. It also integrates and controls instrumentation in ProteomIQ®, centralizing all data and results into an IBM DB2 relational database. It thus forms the basis of a system for automating protein analysis and identification in a proteomic project. BioinformatIQ®, in conjunction with the ProteomIQ® platform, has been used to manage data acquisition, storage, and analysis for discovery projects at Proteome Systems and in the facilities of our customers. One example is the analysis of human plasma, which is readily obtained and is already commonly used for diagnostic and prognostic purposes in medicine. Changes in the protein expression in the plasma may also be linked with overall systemic changes rather than changes in a particular tissue. Several of our discovery programs involve the comparison of plasma obtained from subjects with a certain disease to the plasma of healthy control subjects. Differences in the protein expression point to marker proteins that may be used in diagnostics to identify the disease, prognostics to monitor or predict the course of the disease, or as drug targets for possible treatment of the disease. Here we show the results of a simple plasma proteomic analysis.